From b324e738b1ac3e3bb1945f50fb40132a9fbc2b5b Mon Sep 17 00:00:00 2001
From: Frederic Lemoine <fredericlemoine@users.noreply.github.com>
Date: Mon, 26 Feb 2024 23:28:08 +0100
Subject: [PATCH] Added options min-len and max-len to gotree brlen setrand

---
 cmd/randbrlen.go       | 11 ++++++++++-
 docs/commands/brlen.md | 16 ++++++++++------
 2 files changed, 20 insertions(+), 7 deletions(-)

diff --git a/cmd/randbrlen.go b/cmd/randbrlen.go
index 94c6832..e58b4f8 100644
--- a/cmd/randbrlen.go
+++ b/cmd/randbrlen.go
@@ -13,6 +13,8 @@ import (
 var setlengthmean float64
 var setlengthmeanMin float64
 var setlengthmeanMax float64
+var setlengthMinLen float64
+var setlengthMaxLen float64
 
 // randbrlenCmd represents the randbrlen command
 var randbrlenCmd = &cobra.Command{
@@ -31,6 +33,9 @@ Two possibilities for the mean:
 if --internal=false is given, it won't apply to internal branches (only external)
 if --external=false is given, it won't apply to external branches (only internal)
 
+if --min-len > 0, it will apply only to branches with length >= min-len
+if --max-len > 0, it will apply only to branches with length <= max-len
+
 `,
 	RunE: func(cmd *cobra.Command, args []string) (err error) {
 		var f *os.File
@@ -61,7 +66,9 @@ if --external=false is given, it won't apply to external branches (only internal
 			}
 
 			for _, e := range tr.Tree.Edges() {
-				if (e.Right().Tip() && brlenexternal) || (!e.Right().Tip() && brleninternal) {
+				if ((e.Right().Tip() && brlenexternal) || (!e.Right().Tip() && brleninternal)) &&
+					(setlengthMinLen == -1 || e.Length() >= setlengthMinLen) &&
+					(setlengthMaxLen == -1 || e.Length() <= setlengthMaxLen) {
 					e.SetLength(gostats.Exp(1.0 / lmean))
 				}
 			}
@@ -78,5 +85,7 @@ func init() {
 	randbrlenCmd.Flags().Float64VarP(&setlengthmean, "mean", "m", 0.1, "Mean of the exponential distribution of branch lengths")
 	randbrlenCmd.Flags().Float64Var(&setlengthmeanMin, "min-mean", 0.001, "Mean of the exponential distribution of branch lengths will be drawn uniformly in the interval [min-mean,max-mean]")
 	randbrlenCmd.Flags().Float64Var(&setlengthmeanMax, "max-mean", 0.05, "Mean of the exponential distribution of branch lengths will be drawn uniformly in the interval [min-mean,max-mean]")
+	randbrlenCmd.Flags().Float64Var(&setlengthMinLen, "min-len", -1, "Applies only to branches having length >= min-length (taken into account iff > 0)")
+	randbrlenCmd.Flags().Float64Var(&setlengthMaxLen, "max-len", -1, "Applies only to branches having length <= max-length (taken into account iff > 0)")
 	randbrlenCmd.PersistentFlags().StringVarP(&outtreefile, "output", "o", "stdout", "Random length output tree file")
 }
diff --git a/docs/commands/brlen.md b/docs/commands/brlen.md
index 229cbc0..a41360f 100644
--- a/docs/commands/brlen.md
+++ b/docs/commands/brlen.md
@@ -87,15 +87,19 @@ Usage:
   gotree brlen setrand [flags]
 
 Flags:
-  -h, --help         help for setrand
-  -m, --mean float   Mean of the exponential distribution of branch lengths (default 0.1)
-  -o, --output string   Random length output tree file (default "stdout")
+  -h, --help             help for setrand
+      --max-len float    Applies only to branches having length <= max-length (taken into account iff > 0) (default -1)
+      --max-mean float   Mean of the exponential distribution of branch lengths will be drawn uniformly in the interval [min-mean,max-mean] (default 0.05)
+  -m, --mean float       Mean of the exponential distribution of branch lengths (default 0.1)
+      --min-len float    Applies only to branches having length >= min-length (taken into account iff > 0) (default -1)
+      --min-mean float   Mean of the exponential distribution of branch lengths will be drawn uniformly in the interval [min-mean,max-mean] (default 0.001)
+  -o, --output string    Random length output tree file (default "stdout")
 
 Global Flags:
+      --external        Applies to external branches (default true)
+      --format string   Input tree format (newick, nexus, phyloxml, or nextstrain) (default "newick")
   -i, --input string    Input tree (default "stdin")
-      --seed    int     Random Seed: -1 = nano seconds since 1970/01/01 00:00:00 (default -1)
-```
-
+      --internal        Applies to internal branches (default true)
 #### Examples
 
 1. Removing branch lengths from a set of 10 trees